From f48201c14b48abf0a20b746257634c1327413155 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <kontrapunkt@uclmail.net>
Date: Wed, 8 Mar 2023 13:54:50 +0100
Subject: [PATCH] Eliminate internal labelling of individual compound lists.
This was causing unnecessary trouble with loading inputs when running
the command line.
---
R/state.R | 7 +++----
1 file changed, 3 insertions(+), 4 deletions(-)
diff --git a/R/state.R b/R/state.R
index 9bec760..ae724f5 100644
--- a/R/state.R
+++ b/R/state.R
@@ -37,13 +37,12 @@ new_state <- function() {
runtime_from_conf <- function(run,envopts,conf) {
lst_cmpl <- conf$compounds$lists
- lst_fn_cmpl <- lapply(names(lst_cmpl),function (nm) {
- bfn_cmpl <- lst_cmpl[[nm]]
+ lst_fn_cmpl <- lapply(lst_cmpl,function (lst) {
+ bfn_cmpl <- lst
fn <- file.path(run$paths$project,bfn_cmpl)
if (!file.exists(fn)) stop("File ", fn, " does not exist in ", run$paths$project," .")
fn
})
- names(lst_fn_cmpl) <- names(lst_cmpl)
run$paths$compounds$lists <- lst_fn_cmpl
run$paths$data = norm_path(file.path(envopts$top_data_dir,conf$paths$data))
@@ -204,7 +203,7 @@ new_project <- function(project,envopts,datatab=NULL,conf=NULL) {
check_file_absent(fn_conf,what="conf-file")
yaml::yaml.load_file(fn_conf)
} else conf
- m$conf$compounds$lists = label_cmpd_lists(m$conf$compounds$lists)
+ ## m$conf$compounds$lists = label_cmpd_lists(m$conf$compounds$lists)
m$run = new_runtime_state(project,envopts=envopts,conf=m$conf)
if (!is.null(datatab)) {
m$input$tab$mzml = datatab
--
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